Magnesium in PDB 5tdm: Tev Cleaved Human Atp Citrate Lyase Bound to 4R-Hydroxycitrate and Adp

All present enzymatic activity of Tev Cleaved Human Atp Citrate Lyase Bound to 4R-Hydroxycitrate and Adp:
2.3.3.8;

The structure of Tev Cleaved Human Atp Citrate Lyase Bound to 4R-Hydroxycitrate and Adp, PDB code: 5tdm was solved by J.Hu, M.E.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.77 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.379, 84.814, 193.869, 90.00, 90.00, 90.00
R / Rfree (%)	21.6 / 28.6

The binding sites of Magnesium atom in the Tev Cleaved Human Atp Citrate Lyase Bound to 4R-Hydroxycitrate and Adp (pdb code 5tdm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Tev Cleaved Human Atp Citrate Lyase Bound to 4R-Hydroxycitrate and Adp, PDB code: 5tdm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Tev Cleaved Human Atp Citrate Lyase Bound to 4R-Hydroxycitrate and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Tev Cleaved Human Atp Citrate Lyase Bound to 4R-Hydroxycitrate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg903 b:90.1 occ:1.00 O3B A:ADP902 1.7 89.2 1.0 HOB3 A:ADP902 1.8 0.0 1.0 O A:HOH1038 1.9 82.1 1.0 O1A A:ADP902 2.2 74.2 1.0 O A:ASN203 2.3 42.9 1.0 O A:HOH1087 2.3 46.4 1.0 OD2 A:ASP216 2.4 46.3 1.0 PB A:ADP902 3.1 70.3 1.0 PA A:ADP902 3.4 51.0 1.0 CG A:ASP216 3.4 46.3 1.0 C A:ASN203 3.4 31.5 1.0 HB3 A:ASN203 3.5 42.9 1.0 O3A A:ADP902 3.5 79.8 1.0 HB3 A:ASP216 3.7 42.0 1.0 HB2 A:ASP216 3.7 42.0 1.0 HD22 A:ASN203 3.7 51.4 1.0 HD3 A:PRO204 3.8 45.4 1.0 CB A:ASP216 3.8 35.0 1.0 ND2 A:ASN203 4.0 42.8 1.0 O2B A:ADP902 4.0 75.0 1.0 CB A:ASN203 4.1 35.8 1.0 O1B A:ADP902 4.2 40.8 1.0 CG A:ASN203 4.2 41.0 1.0 HO3' A:ADP902 4.2 0.8 1.0 H5'2 A:ADP902 4.3 0.2 1.0 HOB2 A:ADP902 4.3 90.0 1.0 O2A A:ADP902 4.3 65.4 1.0 N A:PRO204 4.3 28.9 1.0 HD21 A:ASN203 4.3 51.4 1.0 HH21 A:ARG66 4.4 51.1 1.0 CD A:PRO204 4.4 37.8 1.0 HOA2 A:ADP902 4.4 78.5 1.0 CA A:ASN203 4.4 33.4 1.0 HD2 A:PRO204 4.4 45.4 1.0 H3' A:ADP902 4.5 0.0 1.0 H A:ASN203 4.5 36.9 1.0 OD1 A:ASP216 4.5 55.6 1.0 O5' A:ADP902 4.6 83.0 1.0 HG12 A:VAL140 4.7 0.7 1.0 O A:HOH1092 4.8 46.7 1.0 N A:ASN203 4.9 30.7 1.0 HB2 A:ASN203 5.0 42.9 1.0 OD1 A:ASN203 5.0 37.7 1.0

Magnesium binding site 2 out of 2 in the Tev Cleaved Human Atp Citrate Lyase Bound to 4R-Hydroxycitrate and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Tev Cleaved Human Atp Citrate Lyase Bound to 4R-Hydroxycitrate and Adp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:63.7 occ:1.00 O B:HOH1009 1.9 50.2 1.0 O3P B:NEP760 2.0 67.5 1.0 O B:HOH1001 2.4 63.7 1.0 O A:HOH1004 2.5 50.1 1.0 HD2 B:NEP760 3.1 89.5 1.0 P B:NEP760 3.5 56.1 1.0 OE1 B:GLU599 3.5 63.5 1.0 OE2 B:GLU599 3.6 0.8 1.0 O6 A:7A2901 3.9 70.7 1.0 H A:GLY282 3.9 72.2 1.0 CD B:GLU599 3.9 91.5 1.0 CD2 B:NEP760 4.0 74.6 1.0 O1P B:NEP760 4.0 55.4 1.0 OE2 A:GLU306 4.0 68.3 1.0 NE2 B:NEP760 4.2 64.3 1.0 HA3 A:GLY282 4.2 74.6 1.0 O2P B:NEP760 4.4 49.3 1.0 OG A:SER308 4.4 59.4 1.0 HG A:SER263 4.5 0.5 1.0 O7 A:7A2901 4.5 74.3 1.0 C5 A:7A2901 4.6 80.8 1.0 N A:GLY282 4.7 60.1 1.0 HA B:NEP760 4.7 69.7 1.0 HB2 A:SER263 4.8 0.8 1.0 HB3 A:SER263 4.8 0.8 1.0 HG A:SER308 4.8 71.2 1.0 CA A:GLY282 4.9 62.2 1.0 O B:GLY759 4.9 77.5 1.0 HZ2 A:LYS265 4.9 0.4 1.0

J.Hu, A.Komakula, M.E.Fraser. Binding of Hydroxycitrate to Human Atp-Citrate Lyase. Acta Crystallogr D Struct V. 73 660 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 28777081
DOI: 10.1107/S2059798317009871